Bevel Shader with a Gradient Texture
Credits to Robin Betts for this, he nailed the issue head-on in the comments. I'm just explaining it a bit more thoroughly with screenshots.

Essentially what is going on is that for all the faces on the larger objects, you've mapped it to have a large bevel. For the smaller ones, you've mapped them to have a smaller bevel.

However, when a small object meets a big object, the face of the larger object is still trying to create a large bevel, while the smaller one is trying to create a small one on the same edge- resulting in that inwards bevel effect.

As you can see in the screenshot below, I've cut additional geometry to surround your smaller objects and moved their UV mapping so that they shared the same bevel width.



Here's a comparison of before/after: